☰ Navigation Tabs
X-Ray Structure of the Murine Norovirus (MNV)-1 Capsid Protein Protruding (P) Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other crystal structure (in house)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 30% PEG 4000, 100 mM Tris, 20 mM sodium chloride, 200 mM lithium sulfate, , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.74 55.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.262 α = 90 b = 105.219 β = 90 c = 84.053 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate mirrors 2008-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 50 86 0.071 10 4.4 24428 24822 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 72 0.273 5 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT crystal structure (in house) 2 32.84 24428 23149 1253 93.26 0.2175 0.21545 0.2145 0.2562 0.2546 RANDOM 28.154
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 19.033 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 9.617 r_scangle_it 4.618 r_scbond_it 3.089 r_angle_refined_deg 2.431 r_mcangle_it 2.431 r_mcbond_it 1.518 r_chiral_restr 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.595 r_dihedral_angle_4_deg 19.033 r_dihedral_angle_3_deg 14.383 r_dihedral_angle_1_deg 9.617 r_scangle_it 4.618 r_scbond_it 3.089 r_angle_refined_deg 2.431 r_mcangle_it 2.431 r_mcbond_it 1.518 r_chiral_restr 0.194 r_bond_refined_d 0.026 r_gen_planes_refined 0.016 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2404 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling